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An agent-based modeling (ABM) framework was developed to support oyster reef restoration efforts in the Caloosahatchee River Estuary located within the encompassing Charlotte Harbor estuarine system, Southwest Florida. The modeling approach is novel for this shallow estuary which experiences heavily managed freshwater inflow known to be an ecological stressor to the estuary's oysters. The aims of the study were to (1) determine the ABM's accuracy in simulating larval dispersal patterns when compared with measured in situ larval settlement data; (2) establish connectivity patterns between various oyster reefs within the estuary; and (3) discover larval transport pathways within the Charlotte Harbor estuarine system. Key characteristics of the ABM, in particular the agents serving as simulated larvae, include settlement behavior and salinity tolerance and associated mortality. The ABM accurately recreated larval dispersal patterns during the peak spawning season, providing fundamental insight into the importance of protecting the furthest upstream oyster reef as a sustained larval source to the downstream reefs. Thus, supporting the effectiveness of using field measurements for the validation of ABMs and subsequently using ABM simulations to bolster future field studies. Ultimately, this study provides an effective, generally applicable, approach to model larval ecology for restoration purposes.

Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 126(1), (2021): e2020JC016771, https://doi.org/10.1029/2020JC016771., Estuaries worldwide have experienced modifications including channel deepening and intertidal reclamation over several centuries, resulting in altered fine sediment routing. Estuaries respond differently based on preexisting geometries, freshwater and sediment supplies, and extents and types of modification. The Coos Bay Estuary in Oregon is a relatively small estuary with complex geometry that has been extensively modified since 1865. A sediment transport model calibrated to modern conditions is used to assess the corresponding changes in sediment dynamics. Over ∼150 years, channel deepening (from ∼6.7 to 11 m), a 12% increase in area, and a 21% increase in volume have led to greater tidal amplitudes, salinity intrusion, and estuarine exchange flow. These changes have reduced current magnitudes, reduced bed stresses, and increased stratification, especially during rainy periods. Historically, fluvially derived sediment was dispersed across broad, deltaic‐style flats and through small tidal channels. Now, river water and sediments are diverted into a dredged navigation channel where an estuarine turbidity maximum (ETM) forms, with modeled concentrations >50 mg/L and measured concentrations >100 mg/L during discharge events. This “new” ETM supplies sediment to proximal embayments in the middle estuary and the shallow flats. Overall, sediment trapping during winter (and high river discharges) has increased more than two‐fold, owing to increased accommodation space, altered pathways of supply, and altered bed stresses and tidal asymmetries. In contrast to funnel‐shaped estuaries with simpler geometries and river‐channel transitions, these results highlight the importance of channel routing together with dredging in enhancing sediment retention and shifting pathways of sediment delivery., The Science Collaborative is funded by the National Oceanic and Atmospheric Administration and managed by the University of Michigan Water Center (NAI4NOS4190145)., 2021-06-14